Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to visualize detailed internal structures. MRI makes use of the property of nuclear magnetic resonance to image nuclei of atoms inside the body. An MRI machine uses a powerful magnetic field to align the magnetization of some atoms in the body, and radio frequency fields to systematically alter the alignment of this magnetization. This causes the nuclei to produce a rotating magnetic field detectable by the scanner, which can be detected and used to construct an image of the scanned area of the body. Strong magnetic field gradients cause nuclei at different locations to rotate at different speeds, and thus three-dimensional spatial information can be obtained by providing gradients in each direction.
MRI can be used to capture a sequence of three-dimensional images acquired over time, for example, to review the response of a given part of the body, such as the brain, to an applied stimulus. In a common embodiment of this form of MRI, the image contrast can be made sensitive to blood oxygenation, and is typically used to image brain tissue. This is most often called blood oxygenation level dependent (BOLD) contrast, and is used for identifying brain regions that are functionally relevant for particular tasks or are functionally related by similar contrast changes (functional MRI). Functional MRI involves the acquisition of a sequence of three-dimensional volumes of images.
In typical practice, the acquisition of several to hundreds of volumes takes place over several minutes, each volume being acquired over a few seconds, resulting in a time series of three-dimensional volumes. Each volume acquisition is most commonly acquired as a stack of two-dimensional slices of images, with each two-dimensional image or images being acquired in 50-200 milliseconds, and with a time delay between some or all of the slices, such that one slice may be acquired near the beginning of the volume acquisition while another slice may be acquired near the end of the volume acquisition. In typical practice, the slices are acquired at time delays that are linearly spaced within the volume acquisition. During the data acquisition, it is possible and in fact very common that the head and brain will move to a different position and orientation. The effect of motion on BOLD signal level is complex and will result in signal changes that are due to the motion and not due to changes in BOLD contrast. These are termed motion artifact signals and the presence of more than only a few hundred microns of motion can result in corrupted data.